gg_seg

As a neuroscience grad student with a background in psychology, I wasn’t permitted to take the somewhat coveted neuroanatomy course that the neuroscience department offered at my undergraduate institution. This course was all the hype! Dissecting sheep brains, carefully studying brain structures with the help of atlases and coming out smelling like formaldehyde (too far?). Point is, I felt clearly disadvantaged given that I am aware of the functioning of structures such as the percuneus, inferior frontal gyrus and fornix but can’t visualize them.

While there are some great software available online, access is limited by one simple problem…. MONEY!!! Just when I was about to buy an atlas, I came across this incredibly cool feature in r that lets you visualize the brain in a 2D and a 3D fashion.

The r package that let’s you do a 2D analysis is called ggseg. From an input standpoint, it is like the ggplot package but uses inbuilt atlases to display the brain from various vantage points.

Stacked Image

This is just a simple stacked image.

ggseg(atlas=“dk”,position = “stacked”) + theme_classic() +

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As you might ahve noticed, the image lacks detail and gives a gross anatomy of the human brain.

A Medial view with the aseg atlas

ggseg(atlas=“aseg”,position = “stacked”) + theme_classic() +

labs(title = “aseg_atlas”, subtitle = “classic theme”)

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Region Fill

You can also add legends and fill areas on the plot according to brain regions.

ggseg(mapping=aes(file=region),colour=“white”)+

scale_fill_brain(“aseg”)+

theme(legend.justification = c(1,0),legend.position = “right”,

legend.text = element_text(size=6))+

guides(fill=guide_legend(ncols=3))

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2D Subcortical Structures

Sub-cortical structures, e.g., basal ganglia, substantia nigra are embedded deep into the brain and can typically be seen after slicing the brain into two halves.

Here, the brain is dissected into coronal sections (anterior and posterior halves) and subcortical structures are labelled.

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Now for the coolest one…

The 3D atlas…

In addition to the arguments taken by a 2D atlas, this takes the arguments of opacity and color for the background

The functionality is especially great for visualizing the sub cortical structures that are buried deep under the cortex. What’s more? it also labels them!You can also zoom or rotate the image and see it from multiple dimensions

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ggseg (atlas = “aseg”,

mapping = aes(fill = region)) +

theme(legend.justification = c(1, 0), legend.position = “bottom” , legend.text = element_text(size = 5)) +

guides(fill = guide_legend(ncol = 3))

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Suffice to say that I won’t be needing an atlas anymore… :)